Group 4 Project Presentation: Gene Expression in bone marrow derived cells in healthy donors and patients with myelodysplastic syndrome

-Tilman Nelissen (s233043) -Thea Rehm Rosholm (s225019) -Edir Sebastian Vidal Castro (s243564) -Nithiyashri Jayashankar (s244356) -Morten Orebo Holmström (s242223)

2024-12-03

Introduction

  • The myelodysplastic syndromes (MDS) are a diverse set of cancers in the bone marrow.
  • The bone marrow consists of several cell types - amongst these hematopoietic stem cells and progenitor cells.
  • Gene expression analysis of specific cell fractions derived from the bone marrow could reveal potential targets of therapy and immune evasive mechanisms.

From: https://www.sigmaaldrich.com/

Materials and methods: Data Retrieval and Cleaning

Flowchart of data aquisition and inital tidying

Methods: Gene Mapping, Cleanup and DESeq2 Analysis

Flowchart of data augmentation

Sample compositions

Distribution of counts

Histogram normalized

Histogram non-normalized

Clustering using PCA on all cells and on HSC

Clustering analysis using K-means (k = 4) compared to umap:

Differential gene expression: All samples and HSC

Differential gene expression across the different cell populations - MDS vs. HD

Conclusion and perspectives

  • Several genes are differentially expressed between healthy donors and patients with MDS in the four analyzed cell populations.

  • Single cell analysis (RNASeq or proteomics) would provide further detail.

  • Differences in expression between the SF3B1/SRSF2 mutants and wild types?

  • More sample/clinical data on MDS samples would allow to analyze these more in deeply and gain more knowledge of differential gene expression between different classes of MDS.

22160 - R for Bio Data Science